The vast, vast majority of science articles follow the same basic pattern: abstract, introduction, methods, results, discussion. * * * There are no stories, no narrative, no amusing anecdotes. * * * Rather, there's just line after line of jargon leaden prose in the passive tense.

Jonah is not particularly pleased by this:

Why can't more science papers break the mold, even a little?
* * *
And why is there a prohibition against good science stories in science journals? Why not take a few sentences and describe where the idea for the experiment came from, or some of the experimental failures along the way, or the most surprising results. I'm not asking for a novel: all I want is an anecdote or two, a few honest insights into the messy reality of the scientific process.

[T]he standard form of a scientific research article is exactly a narrative or story.
We understand this, that and the other thing about blah, blah, blah. Based on this understanding, we pose the following hypothesis. In order to test this hypothesis, we did x, y, and z, and observed a, b, c. On the basis of these observations, we conclude that blah, blah, blah, thus supporting/rejecting this hypothesis. This implies blah, thus suggesting the importance of blah, blah, blah, and leading to the following future studies.
What is this but a narrative or story? And the funny thing is that it is almost always a completed fabricated story. Most of the time, and experiment is performed after saying "let's see what happens if we do x to y". After you see the results, you go back and make up a hypothesis that the experiment tested, and which the results either support or exclude.
All this "in order to test this hypothesis, we did this experiment" is almost always a total lie.

That's a great point about the inherent dishonesty of the scientific paper format. It's funny how science papers still subscribe to a fictional version of the scientific process taught to fifth graders. (First, generate a hypothesis. Then, design an experiment to test the hypothesis...) So yes, I guess you're right: science papers do present a narrative, they just tend to be incredibly dry, tedious and false. Not a great combination.

Maybe this is an issue for non-scientists reading scientific research, but it is a non-issue for the scientists working in a field themselves. The structure is very formal and rigid, so that the maximum amount of information can be accessed by the reader as efficiently and predictably as possible.
Scientific research papers are not meant to be read through like a magazine article. They are meant to provide a highly structured format for presentation of a ton of detailed information, so that a user of that information can home in on exactly what they want as quickly and easily as possible.
And the fact that the narrative is a lie is completely irrelevant. Everyone knows it's a lie. It's just a rhetorical device that allows for the experimental results to be placed in an appropriate conceptual context and related to existing work in a field.
Personally, I would be very annoyed with an author who deviated from this very strict ritualized structure for a scientific paper, because it would make my work more difficult. Don't mess with this!
I do not want to have to sift through "where the idea for the experiment came from, or some of the experimental failures along the way, or the most surprising results" nor "an anecdote or two, a few honest insights into the messy reality of the scientific process". Scientists are aware of the existence of all this crap, and it is fine for discussion over beers, but it would just get in the way in a scientific research paper.
Where the writing of scientific papers could be dramatically improved is not in their top-level rhetorical and literary structure, but in the construction of decent clear English sentences and paragraphs.
UPDATE: Oh, and in relation to the "passive tense", this may have been an issue in the past, but it is pretty much just a red herring at this point. I am aware of no journal that copy edits prose to introduce passive tense to replace "we did this, and then we did that" with "this was done, and then that was done". The vast majority of contemporary scientific articles I read--and all of the ones that emanate from my lab--are written with a bog-standard mix of active and passive voice, just like any other narrative writing.

It *is* fun when I do have to dig in the library archives and read one of those old-skool papers with 30 pages of rambling narrative and expostulation, but only because it's maybe once a year. Those papers certainly show how slow-paced research used to be.

just giving the facts does not necessarily have to be boring:http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jo00800a036
but I do recognize the point the student makes about revealing other aspects of the work, and having more of a narrative description of the background and all that other stuff is very useful for 3 reasons: (1) multi-disciplinary research, where it would simplify reading stuff from other fields - I find when looking at an unfamiliar subfield, that Perspectives and Reviews that take a narrative standpoint are great educational tools and mean that when I talk to someone from that other sub-field, I can start from a point of non-ignorance, (2) educating non-scientists about the process and significance of research, and (3) educating patients about the process of basic biomedical research and how it may relate to future clinical progress.

Background story and anecdotes should be in a blog post. Ideally, the paper and the blog post would link to each other directly. I did that for all of my papers - the paper and the post are written in very different format and style, having different audiences in mind. And yes, I also like to sometimes read an old 30-page paper. And reviews are certainly presented in a different, more flowing, manner.

Word.
It surprised me somewhat in writing my first paper as a grad student about how much the order of expts in the paper was in no way related to their chronological order. But quickly that disappeared, and as all working scientists, I realized that the "deductive" structure of the typical paper, where you're not supposed to draw conclusions in the Results, is so bogus. Implicit in the expts you actually did is the hypothesis (well formed, or more like, hmm, what would happen if we did this) so why the facade. In fact, now I get annoyed when there's too little conclusions drawn during the presentation of the results.
And I'm all for the boring aspect of papers. Just the facts please. Fun stories about the actual practice of science are good for blogs though.

D'oh, I forgot! I also loves me some old papers.
Not necessarily for any particular style considerations, but more for appreciating the giantness of those who came before us.
I can think of a few papers from 1952 in particular. From J. Physiol. By a couple of blokes named Hodgkin and Huxley. Yeah that's right!

I realized that the "deductive" structure of the typical paper, where you're not supposed to draw conclusions in the Results, is so bogus.

I don't ever follow this "rule" with papers emanating from my lab. Each section in the results ends with at least one sentence laying out the conceptual conclusion that follows from the experiments presented in that section, and even sometimes briefly relates it to the existing literature. I have never received a single reviewer or editor complaint about this, or any other aspect of the writing and structure of my papers.
I can't say I've noticed if other people frequently do this or not.

Papers flow much better if you have a few discussion points in the results. It helps bridge the experiments. Most reviewers don't pay it any heed, however, I did have one particular reviewer who was OUTRAGED that I did this very thing. It was amusing, because the other reviewer requested more of the same behavior. Ahhh, nothing like dualing reviewers.

I'm fine with the formalized structure of scientific papers...but I do wish there was some venue for "we tried this, but it didn't work" so that we didn't spend so much time reinventing the [square] wheel. Maybe some sort of online space where there could be short reports: "We thought that X was correlated with Y, but we tested it with dataset Z, and the r2 sucked." They could even be anonymous so there were no career repercussions.

ScienceWoman -- I agree, but nowadays you can just post results (or non-results) that aren't worth a journal paper on your website, and there's some chance that the next person who tries to do the same thing will do a web search and find your report or blog post or whatever.
P.S. -- There's an anecdote in Jon Beckwith's autobiography about how he tried to write a paper using the true narrative of the work instead of the standard style. It was rejected multiple times, and then published in PNAS without peer review (he's a member of the academy). I bet it would have been easier to read if it was written the normal way.

the advantage of a paper written in the standard way is that it makes matters much easier for the reader, you just know where to look if you need the essence of the study, without having to read every single word. it may be dry, alright, but the standard form still seems like the most efficient way of communicating findings.
and drawing a mini-conclusion for each result is useful too i think, with the actual discussion being reserved for the most important results, the bigger picture and future implications.
as to negative findings, mishaps and the like - isn't that what the supplement is (/should be) for?

I have to disagree with the idea that the narrative is a lie, although I expect this is overstated to make a point. I expect most papers (at east my lab's papers) actually do derive from a we wanted to understand this, so we did x, y, and z, from which we learned m and n, which led us to hypothesize that p and q, so we did experiment....
I will agree that the paper is not historically accurate. You describe results where they are logical with the main points of the paper, which may not reflect the order the experiments were done. I would not consider this a "lie."
Regardless, excellent post PP, papers are indeed narratives and please don't fuck with the system. If I want lots of extraneous words and more flowery language to mix it up, Ill go read one of the many books I have sitting next to my bed that I read for pleasure/recreation. Precision is key, if you see a 42 kilodalton protein on your protein gel say that, dont say "We were excited to see that protein moved through the gel to a spot virtually indistinguishable from that well studied protein actin. Considering how important actin is to so many basic cellular functions, we could not help but wonder, was our protein important in many cellular functions."
Regarding sciencewoman's negative data. Much negative data can be included, often as a "data not shown" statement, which led us to consider blah blah and blah. I think its a essentially an urban legend that you can't publish negative data (although I agree you cannot publish ONLY negative data). Its simple to find papers where two models are considered and support for one model over another comes from negative data. Also, I think most negative data is positive data if you set up the narrative of your experiment differently. And finally, I expect this is well understood, but I always like to make it explicitly clear, negative data should never be confused with the "experiment didn't work."
Conclusions in the results. Isn't that the norm? Not overarching or more esoteric conclusions (these are positioned in the discussion), but we wanted to know this, we did this experiment and saw this. Thus, yadda yadda yadda

Perhaps this is why writing grants is so much harder than writing up empirical work? Because one is, to some extent, required to actually work through to a specific hypothesis? One that is a 'sure bet'?
I mean, i was an english major as an undergrad. I LOVE working within the rigidity of the standard narrative format for writing up data, and making up something that works to connect the actual results to some of the problems i care about. I just hate pretending that i go through some deeply logical process to derive hypotheses from theories, for the sake of getting funds.